data_7M8V
#
_model_server_result.job_id            tFWQ-91EGsyULuCngzYBqw 
_model_server_result.datetime_utc      '2024-11-28 20:54:33' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          7m8v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":601}' 
#
_entry.id    7M8V 
#
_exptl.entry_id    7M8V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              227.237 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-[(4R,5R)-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-5-yl]-3-fluorobenzonitrile 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         82.807 
_cell.angle_beta          70.033 
_cell.angle_gamma         79.369 
_cell.entry_id            7M8V 
_cell.length_a            123.946 
_cell.length_b            126.423 
_cell.length_c            174.928 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7M8V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
? monomeric 1 author_defined_assembly 7 
? monomeric 1 author_defined_assembly 8 
? monomeric 1 author_defined_assembly 9 
? monomeric 1 author_defined_assembly 10 
? monomeric 1 author_defined_assembly 11 
? monomeric 1 author_defined_assembly 12 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,M,N,KA 1 1 
B,O,P,LA 2 1 
C,Q,R,MA 3 1 
D,S,T 4 1 
E,U,V,NA 5 1 
F,W,X,OA 6 1 
G,Y,Z,PA 7 1 
H,AA,BA 8 1 
I,CA,DA 9 1 
J,EA,FA 10 1 
K,GA,HA 11 1 
L,IA,JA 12 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W N N 
? 2 Y N N 
? 2 AA N N 
? 2 CA N N 
? 2 EA N N 
? 2 GA N N 
? 2 IA N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 M N15 YSY . A YSY 601 1_555 N FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc2 B SG CYS 427 B CYS 450 1_555 P FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? 
metalc ? metalc3 O N15 YSY . B YSY 601 1_555 P FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc4 C SG CYS 427 C CYS 450 1_555 R FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc5 Q N15 YSY . C YSY 601 1_555 R FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc6 S N15 YSY . D YSY 601 1_555 T FE HEM . D HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc7 U N15 YSY . E YSY 601 1_555 V FE HEM . E HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc8 W N15 YSY . F YSY 601 1_555 X FE HEM . F HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc9 Y N15 YSY . G YSY 601 1_555 Z FE HEM . G HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc10 AA N15 YSY . H YSY 601 1_555 BA FE HEM . H HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc11 CA N15 YSY . I YSY 601 1_555 DA FE HEM . I HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc12 EA N15 YSY . J YSY 601 1_555 FA FE HEM . J HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc13 GA N15 YSY . K YSY 601 1_555 HA FE HEM . K HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc14 IA N15 YSY . L YSY 601 1_555 JA FE HEM . L HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
#
_chem_comp.formula           'C13 H10 F N3' 
_chem_comp.formula_weight    227.237 
_chem_comp.id                YSY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-[(4R,5R)-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-5-yl]-3-fluorobenzonitrile 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Osilodrostat 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C14 N15 YSY sing 458 n y 
C14 C13 YSY doub 459 n y 
N15 C16 YSY doub 460 n y 
C13 C12 YSY sing 461 n n 
C13 N17 YSY sing 462 n y 
C12 C11 YSY sing 463 n n 
C16 N17 YSY sing 464 n y 
N17 C10 YSY sing 465 n n 
C11 C10 YSY sing 466 n n 
C10 C06 YSY sing 467 n n 
C05 C04 YSY doub 468 n y 
C05 C06 YSY sing 469 n y 
C04 C03 YSY sing 470 n y 
C06 C07 YSY doub 471 n y 
C07 F08 YSY sing 472 n n 
C07 C09 YSY sing 473 n y 
C03 C09 YSY doub 474 n y 
C03 C02 YSY sing 475 n n 
C02 N01 YSY trip 476 n n 
C10 H101 YSY sing 477 n n 
C04 H041 YSY sing 478 n n 
C05 H051 YSY sing 479 n n 
C09 H091 YSY sing 480 n n 
C11 H111 YSY sing 481 n n 
C11 H112 YSY sing 482 n n 
C12 H121 YSY sing 483 n n 
C12 H122 YSY sing 484 n n 
C14 H141 YSY sing 485 n n 
C16 H161 YSY sing 486 n n 
#
_atom_sites.entry_id                     7M8V 
_atom_sites.fract_transf_matrix[1][1]    0.008068 
_atom_sites.fract_transf_matrix[1][2]    -0.001514 
_atom_sites.fract_transf_matrix[1][3]    -0.002836 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008048 
_atom_sites.fract_transf_matrix[2][3]    -0.000543 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.006096 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
M 2 YSY A 1 601 602 YSY LIG . 
N 3 HEM A 1 602 601 HEM HEM . 
O 2 YSY B 1 601 602 YSY LIG . 
P 3 HEM B 1 602 601 HEM HEM . 
Q 2 YSY C 1 601 602 YSY LIG . 
R 3 HEM C 1 602 601 HEM HEM . 
S 2 YSY D 1 601 602 YSY LIG . 
T 3 HEM D 1 602 601 HEM HEM . 
U 2 YSY E 1 601 602 YSY LIG . 
V 3 HEM E 1 602 601 HEM HEM . 
W 2 YSY F 1 601 602 YSY LIG . 
X 3 HEM F 1 602 601 HEM HEM . 
Y 2 YSY G 1 601 602 YSY LIG . 
Z 3 HEM G 1 602 601 HEM HEM . 
AA 2 YSY H 1 601 602 YSY LIG . 
BA 3 HEM H 1 602 601 HEM HEM . 
CA 2 YSY I 1 601 602 YSY LIG . 
DA 3 HEM I 1 602 601 HEM HEM . 
EA 2 YSY J 1 601 602 YSY LIG . 
FA 3 HEM J 1 602 601 HEM HEM . 
GA 2 YSY K 1 601 602 YSY LIG . 
HA 3 HEM K 1 602 601 HEM HEM . 
IA 2 YSY L 1 601 602 YSY LIG . 
JA 3 HEM L 1 602 601 HEM HEM . 
KA 4 HOH A 1 701 1 HOH HOH . 
LA 4 HOH B 1 701 2 HOH HOH . 
MA 4 HOH C 1 701 3 HOH HOH . 
NA 4 HOH E 1 701 4 HOH HOH . 
OA 4 HOH F 1 701 5 HOH HOH . 
PA 4 HOH G 1 701 6 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C10 YSY . . . Y 2 91.326 -84.284 -87.718 1 56.96 ? C10 YSY 601 G 1 
HETATM 2 C C13 YSY . . . Y 2 92.264 -84.396 -89.925 1 50.37 ? C13 YSY 601 G 1 
HETATM 3 C C02 YSY . . . Y 2 93.794 -85.251 -82.554 1 55.49 ? C02 YSY 601 G 1 
HETATM 4 C C03 YSY . . . Y 2 93.215 -85.028 -83.813 1 51.36 ? C03 YSY 601 G 1 
HETATM 5 C C04 YSY . . . Y 2 93.817 -85.412 -85.018 1 55.43 ? C04 YSY 601 G 1 
HETATM 6 C C05 YSY . . . Y 2 93.19 -85.163 -86.253 1 55.74 ? C05 YSY 601 G 1 
HETATM 7 C C06 YSY . . . Y 2 91.946 -84.525 -86.357 1 53.65 ? C06 YSY 601 G 1 
HETATM 8 C C07 YSY . . . Y 2 91.379 -84.161 -85.15 1 52.02 ? C07 YSY 601 G 1 
HETATM 9 C C09 YSY . . . Y 2 91.969 -84.392 -83.898 1 53.82 ? C09 YSY 601 G 1 
HETATM 10 C C11 YSY . . . Y 2 91.595 -82.842 -88.216 1 56.62 ? C11 YSY 601 G 1 
HETATM 11 C C12 YSY . . . Y 2 92.148 -82.945 -89.662 1 59.32 ? C12 YSY 601 G 1 
HETATM 12 C C14 YSY . . . Y 2 92.662 -85.349 -90.847 1 55.6 ? C14 YSY 601 G 1 
HETATM 13 C C16 YSY . . . Y 2 91.93 -86.469 -89.109 1 54.2 ? C16 YSY 601 G 1 
HETATM 14 F F08 YSY . . . Y 2 90.166 -83.538 -85.223 1 52.1 ? F08 YSY 601 G 1 
HETATM 15 N N01 YSY . . . Y 2 94.284 -85.44 -81.486 1 60.76 ? N01 YSY 601 G 1 
HETATM 16 N N15 YSY . . . Y 2 92.449 -86.624 -90.325 1 53.52 ? N15 YSY 601 G 1 
HETATM 17 N N17 YSY . . . Y 2 91.789 -85.124 -88.81 1 53 ? N17 YSY 601 G 1 
HETATM 18 H H101 YSY . . . Y 2 90.357 -84.332 -87.71 1 68.55 ? H101 YSY 601 G 1 
HETATM 19 H H041 YSY . . . Y 2 94.643 -85.835 -84.959 1 66.72 ? H041 YSY 601 G 1 
HETATM 20 H H051 YSY . . . Y 2 93.599 -85.425 -87.046 1 67.08 ? H051 YSY 601 G 1 
HETATM 21 H H091 YSY . . . Y 2 91.611 -84.16 -83.071 1 64.79 ? H091 YSY 601 G 1 
HETATM 22 H H111 YSY . . . Y 2 90.769 -82.335 -88.17 1 68.14 ? H111 YSY 601 G 1 
HETATM 23 H H112 YSY . . . Y 2 92.217 -82.411 -87.61 1 68.14 ? H112 YSY 601 G 1 
HETATM 24 H H121 YSY . . . Y 2 91.545 -82.492 -90.272 1 71.39 ? H121 YSY 601 G 1 
HETATM 25 H H122 YSY . . . Y 2 92.996 -82.477 -89.716 1 71.39 ? H122 YSY 601 G 1 
HETATM 26 H H141 YSY . . . Y 2 93.025 -85.352 -91.703 1 66.92 ? H141 YSY 601 G 1 
HETATM 27 H H161 YSY . . . Y 2 91.728 -87.231 -88.615 1 65.24 ? H161 YSY 601 G 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           132 
_model_server_stats.create_model_time_ms    341 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#